Merge branch 'main' into electron_maxstep

.github/workflows/ci.yml

@@ -13,7 +13,6 @@ concurrency:
 
 env:
     FORCE_COLOR: 1
-    UV_VERSION: 0.3.0
 
 jobs:
 
@@ -45,7 +44,9 @@ jobs:
                   python-version: ${{ matrix.python-version }}
 
             - name: Install uv
-              run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/${{ env.UV_VERSION }}/uv-installer.sh | sh
+              uses: astral-sh/setup-uv@v1
+              with:
+                  version: 0.4.7
 
             - name: Install package
               run: uv pip install --system -e .[dev] aiida-core==${{ matrix.aiida-core-version }}

.gitignore

@@ -7,7 +7,7 @@
 build/
 export/
 .do-not-setup-on-localhost
-
+.mypy_cache/
 
 # Sphinx documentation
 docs/html

Dockerfile

@@ -1,6 +1,6 @@
 # syntax=docker/dockerfile:1
-ARG FULL_STACK_VER=2024.1021
-ARG UV_VER=0.2.27
+ARG FULL_STACK_VER=2024.1022
+ARG UV_VER=0.4.7
 ARG QE_VER=7.2
 ARG QE_DIR=/opt/conda/envs/quantum-espresso-${QE_VER}
 

pyproject.toml

@@ -8,12 +8,16 @@ build-backend = "setuptools.build_meta"
 [tool.pytest.ini_options]
 addopts = '--strict-config --strict-markers --durations=30 --durations-min=1 -ra'
 filterwarnings = [
-    'ignore:Object of type .* not in session, .* operation along .* will not proceed:',
+    # This is needed since SQLAlchemy 2.0, see
+    # https://github.com/aiidalab/aiidalab-widgets-base/issues/605
+    'ignore:Object of type.*not in session,.*operation along.*will not proceed:',
     'ignore:Creating AiiDA configuration:UserWarning:',
     'ignore:metadata.*traitlets.traitlets.Unicode object:DeprecationWarning:',
     # For some reason we get this error, see
     # https://github.com/aiidalab/aiidalab-widgets-base/issues/551
     'ignore:Exception ignored in:pytest.PytestUnraisableExceptionWarning:_pytest',
+    # This popped up in spglib 2.5. Since we still try to support spglib v1,
+    "ignore:dict interface.*is deprecated.Use attribute interface:DeprecationWarning:",
 ]
 
 [tool.ruff]

qe.ipynb

@@ -24,6 +24,17 @@
     "load_profile();"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from aiidalab_widgets_base.utils.loaders import load_css\n",
+    "\n",
+    "load_css(css_path=\"src/aiidalab_qe/app/static/styles\")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -36,21 +47,24 @@
     "\n",
     "    sys.modules[\"pybel\"] = __import__(\"openbabel\", globals(), locals(), [\"pybel\"]).pybel\n",
     "except Exception:\n",
-    "    pass\n",
+    "    pass"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from IPython.display import display\n",
     "\n",
-    "import urllib.parse as urlparse\n",
-    "from datetime import datetime\n",
+    "from aiidalab_qe.app.wrapper import AppWrapperContoller, AppWrapperModel, AppWrapperView\n",
     "\n",
-    "import ipywidgets as ipw\n",
-    "from importlib_resources import files\n",
-    "from IPython.display import display\n",
-    "from jinja2 import Environment\n",
+    "model = AppWrapperModel()\n",
+    "view = AppWrapperView()\n",
+    "controller = AppWrapperContoller(model, view)\n",
     "\n",
-    "from aiidalab_qe.app import App, static\n",
-    "from aiidalab_qe.version import __version__\n",
-    "from aiidalab_widgets_base.bug_report import (\n",
-    "    install_create_github_issue_exception_handler,\n",
-    ")"
+    "display(view)"
    ]
   },
   {
@@ -59,37 +73,38 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "env = Environment()\n",
+    "import urllib.parse as urlparse\n",
     "\n",
-    "template = files(static).joinpath(\"welcome.jinja\").read_text()\n",
-    "style = files(static).joinpath(\"style.css\").read_text()\n",
-    "welcome_message = ipw.HTML(env.from_string(template).render(style=style))\n",
-    "current_year = datetime.now().year\n",
-    "footer = ipw.HTML(\n",
-    "    f'<p style=\"text-align:right;\">Copyright (c) {current_year} AiiDAlab team &#8195Version: {__version__}</p>'\n",
+    "from aiidalab_qe.app.main import App\n",
+    "from aiidalab_widgets_base.bug_report import (\n",
+    "    install_create_github_issue_exception_handler,\n",
+    ")\n",
+    "\n",
+    "install_create_github_issue_exception_handler(\n",
+    "    view.output,\n",
+    "    url=\"https://github.com/aiidalab/aiidalab-qe/issues/new\",\n",
+    "    labels=(\"bug\", \"automated-report\"),\n",
     ")\n",
     "\n",
     "url = urlparse.urlsplit(jupyter_notebook_url)  # noqa F821\n",
     "query = urlparse.parse_qs(url.query)\n",
     "\n",
-    "\n",
     "app_with_work_chain_selector = App(qe_auto_setup=True)\n",
     "# if a pk is provided in the query string, set it as the value of the work_chain_selector\n",
     "if \"pk\" in query:\n",
     "    pk = int(query[\"pk\"][0])\n",
     "    app_with_work_chain_selector.work_chain_selector.value = pk\n",
     "\n",
-    "output = ipw.Output()\n",
-    "install_create_github_issue_exception_handler(\n",
-    "    output,\n",
-    "    url=\"https://github.com/aiidalab/aiidalab-qe/issues/new\",\n",
-    "    labels=(\"bug\", \"automated-report\"),\n",
-    ")\n",
-    "\n",
-    "with output:\n",
-    "    display(welcome_message, app_with_work_chain_selector, footer)\n",
-    "\n",
-    "display(output)"
+    "view.main.children = [app_with_work_chain_selector]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "controller.enable_toggles()"
    ]
   }
  ],

setup.cfg

@@ -27,7 +27,7 @@ install_requires =
     aiida-core~=2.2,<3
     Jinja2~=3.0
     aiida-quantumespresso~=4.6
-    aiidalab-widgets-base[optimade]~=2.2.0,<2.4.0
+    aiidalab-widgets-base[optimade]==2.3.0a2
     aiida-pseudo~=1.4
     filelock~=3.8
     importlib-resources~=5.2
@@ -47,7 +47,8 @@ dev =
 
 [options.package_data]
 aiidalab_qe.app.parameters = qeapp.yaml
-aiidalab_qe.app.static = *
+aiidalab_qe.app.static.styles = *.css
+aiidalab_qe.app.static.templates = *.jinja
 aiidalab_qe.app.structure.examples = *
 aiidalab_qe.plugins.xas = pseudo_toc.yaml
 

src/aiidalab_qe/app/__init__.py

@@ -1,7 +1 @@
 """Package for the AiiDAlab QE app."""
-
-from .main import App
-
-__all__ = [
-    "App",
-]

src/aiidalab_qe/app/result/summary_viewer.py

@@ -154,11 +154,11 @@ def _generate_report_html(report):
     """Read from the bulider parameters and generate a html for reporting
     the inputs for the `QeAppWorkChain`.
     """
-    from importlib import resources
+    from importlib.resources import files
 
     from jinja2 import Environment
 
-    from aiidalab_qe.app import static
+    from aiidalab_qe.app.static import styles, templates
 
     def _fmt_yes_no(truthy):
         return "Yes" if truthy else "No"
@@ -169,8 +169,8 @@ def _fmt_yes_no(truthy):
             "fmt_yes_no": _fmt_yes_no,
         }
     )
-    template = resources.read_text(static, "workflow_summary.jinja")
-    style = resources.read_text(static, "style.css")
+    template = files(templates).joinpath("workflow_summary.jinja").read_text()
+    style = files(styles).joinpath("style.css").read_text()
     report = {key: value for key, value in report.items() if value is not None}
 
     return env.from_string(template).render(style=style, **report)

src/aiidalab_qe/app/result/workchain_viewer.py

@@ -1,6 +1,6 @@
 import shutil
 import typing as t
-from importlib import resources
+from importlib.resources import files
 from pathlib import Path
 from tempfile import TemporaryDirectory
 
@@ -14,7 +14,7 @@
 from aiida.cmdline.utils.common import get_workchain_report
 from aiida.common import LinkType
 from aiida.orm.utils.serialize import deserialize_unsafe
-from aiidalab_qe.app import static
+from aiidalab_qe.app.static import styles, templates
 from aiidalab_qe.app.utils import get_entry_items
 from aiidalab_widgets_base import ProcessMonitor, register_viewer_widget
 from aiidalab_widgets_base.viewers import StructureDataViewer
@@ -175,8 +175,8 @@ def __init__(self, node, export_dir=None, **kwargs):
             )
             final_calcjob = self._get_final_calcjob(node)
             env = Environment()
-            template = resources.read_text(static, "workflow_failure.jinja")
-            style = resources.read_text(static, "style.css")
+            template = files(templates).joinpath("workflow_failure.jinja").read_text()
+            style = files(styles).joinpath("style.css").read_text()
             output = ipw.HTML(
                 env.from_string(template).render(
                     style=style,

src/aiidalab_qe/app/static/styles/README.md

@@ -0,0 +1,13 @@
+# Stylesheets for the Quantum ESPRESSO app
+
+This folder contains `css` stylesheets. These can be loaded from the styles folder using
+
+```python
+from aiidalab_widgets_base.utils.loaders import load_css
+
+load_css(css_path="src/aiidalab_qe/app/static/styles")  # load all stylesheets in the styles folder
+
+# or
+
+load_css(css_path="src/aiidalab_qe/app/static/styles/<stylesheet>.css") # load a single stylesheet
+```

src/aiidalab_qe/app/static/styles/custom.css

@@ -0,0 +1,48 @@
+/*
+  Override Jupyter width limitation to
+  make apps take full notebook width
+*/
+.output_subarea {
+  max-width: none !important;
+}
+/* end override */
+
+.app-header {
+  margin-bottom: 1em;
+}
+
+.logo {
+  text-align: center;
+}
+
+#subtitle {
+  text-align: center;
+  font-style: italic;
+}
+
+.info-toggles {
+  margin: 0 auto;
+}
+.info-toggles button {
+  width: 100px;
+  margin: 1em 0.5em;
+}
+.info-toggles button:focus {
+  outline: none !important;
+}
+
+.guide ol {
+  list-style: none;
+}
+.guide p:not(:last-of-type) {
+  margin-bottom: 0.5em;
+}
+
+#loading {
+  text-align: center;
+  font-size: large;
+}
+
+footer {
+  text-align: right;
+}

src/aiidalab_qe/app/static/styles/infobox.css

@@ -0,0 +1,15 @@
+.info-box {
+  display: none;
+  margin: 2px;
+  padding: 1em;
+  border: 3px solid orangered;
+  background-color: #ffedcc;
+  border-radius: 1em;
+  -webkit-border-radius: 1em;
+  -moz-border-radius: 1em;
+  -ms-border-radius: 1em;
+  -o-border-radius: 1em;
+}
+.info-box p {
+  line-height: 24px;
+}

src/aiidalab_qe/app/static/templates/about.jinja

@@ -0,0 +1,10 @@
+<div class="about">
+  <p>
+    The <a href="https://www.quantum-espresso.org/" target="_blank">Quantum ESPRESSO</a> app
+    (or QE app for short) is a graphical front end for calculating materials properties using
+    Quantum ESPRESSO (QE). Each property is calculated by workflows powered by the
+    <a href="https://www.aiida.net/" target="_bland"> AiiDA engine</a>, and maintained in the
+    <a href="https://aiida-quantumespresso.readthedocs.io/en/latest/" target="_blank">aiida-quantumespresso plugin</a> and many other plugins developed by the community.
+    for AiiDA.
+  </p>
+</div>

src/aiidalab_qe/app/static/templates/guide.jinja

@@ -0,0 +1,42 @@
+<div class="guide">
+  <p>
+    The QE app allows you to calculate properties in a simple 4-step process:
+  </p>
+
+  <ol>
+    <li>
+      🔍 <strong>Step 1:</strong> Select the structure you want to run.
+    </li>
+    <li>
+      ⚙️ <strong>Step 2:</strong> Select the properties you are interested in.
+    </li>
+    <li>
+      💻 <strong>Step 3:</strong> Choose the computational resources you want to run on.
+    </li>
+    <li>
+      🚀 <strong>Step 4:</strong> Submit your workflow.
+    </li>
+  </ol>
+
+  <p>
+    New users can go straight to the first step and select their structure.
+  </p>
+
+  <p>
+    Completed workflows can be selected at the top of the app.
+  </p>
+
+  <p>
+    You can also check out the
+    <a href="https://aiidalab-qe.readthedocs.io/tutorials/basic.html" target="_blank">basic</a> tutorial to get started
+    with the Quantum ESPRESSO app, or try out the
+    <a href="https://aiidalab-qe.readthedocs.io/tutorials/advanced.html" target="_blank">advanced</a> tutorial to learn
+    additional features offered by the app.
+  </p>
+
+  <p>
+    For a more in-depth dive into the app's features, please refer to the
+    <a href="https://aiidalab-qe.readthedocs.io/howto/index.html" target="_blank">how-to guides</a>.
+  </p>
+  </p>
+</div>

src/aiidalab_qe/app/static/workflow_failure.jinja → src/aiidalab_qe/app/static/templates/workflow_failure.jinja

@@ -1,9 +1,3 @@
-<head>
-  <style>
-    {{ style }}
-  </style>
-</head>
-
 <body>
 
 <div class="alert alert-danger error-container">